The RAF Search and Rescue pilot wrote a letter to the mountain rescue volunteers telling them how 'proud' and 'humbled' he was by their efforts to find the five-year-old who went missing in Machynlleth, Mid-Wales, on October 1.
His tribute came as police revealed they had switched their search from the river and waterways surrounding the village to focus on the dense woodland.
In his letter the Duke of Cambridge wrote: "I am time and again made to feel so proud and so humbled by our rescue teams - the lengths you go to in your work, your commitment and dedication to the job, and your extraordinary professionalism.
"This was as evident as ever in the recent search for little April Jones, who was so awfully taken away from her family.
"These high profile cases are just a reminder to us all of what the mountain rescue teams do day in, day out.
"I am sure that the search for April must have been the hardest of its kind. "I know that you did everything in your power to find her.
"I cannot commend you highly enough for your unbelievable perseverance, grit and sheer hard work - we are all so lucky to have people like you in our communities."
Prince William enjoys a close relationship with the rescue volunteers, in both his role as a pilot and the royal patron of the Mountain Rescue England and Wales charity.
The Duke of Cambridge and his team from RAF Valley in Anglesey were on constant standby to help find April's body. It has now been over six weeks since she disappeared from Bryn-y-Gog housing estate in Machynlleth, Wales.
Superintendent Ian John, of Dyfed-Powys Police, said the 150-strong search team is now focusing on the 6,000 hectares of woodland surrounding the river.
"We've still got a number of search areas to investigate, but at the moment teams are primarily working in the Dyfi Forest," he said.
"We are not searching the river actively now. The coastguard have stopped doing that, they have adequately searched the water as much as they can.
"Instead, it's primarily the woodland areas, the old slate quarries and the fields which are the main focus of the operation now.
"We are not searching weekends anymore because the officers all need to rest, but we are still working at an intensive level."
Local man Mark Bridger, 46, has been charged with her murder and is due to appear in court on January 11.